COMPARATIVE MULTI-OMICS ANALYSIS OF BACTERIAL AND FUNGAL ENDOPHYTES FOR ALLEVIATING COMBINED SALINITY AND CADMIUM STRESS

Abstract

The concurrent occurrence of soil salinization and cadmium contamination poses a severe threat to global agricultural productivity, creating synergistic phytotoxic effects that overwhelm plant intrinsic defense mechanisms. Endophytic microorganisms have emerged as critical biological regulators that enhance host tolerance through diverse molecular strategies; however, the comparative functional roles of bacterial versus fungal endophytes under combined stress remain inadequately characterized. This review presents a comprehensive comparative multi-omics analysis of bacterial and fungal endophytes in mitigating simultaneous salinity and cadmium stress. Bacterial endophytes, predominantly Bacillus, Pseudomonas, and Enterobacter species, demonstrate superior capabilities in biomass preservation, active sodium extrusion via Na⁺/H⁺ antiporters, ACC deaminase-mediated ethylene suppression, and nitrogen fixation. Conversely, fungal endophytes including Epichloë, Trichoderma, and Dark Septate Endophytes excel in osmotic adjustment through compatible solute accumulation, profound antioxidant system induction, and mycelial cadmium biosorption. Through integrated multi-omics approaches encompassing genomics, transcriptomics, proteomics, metabolomics, and ionomics we elucidate the systems-level molecular dialogue governing plant-endophyte symbiosis. Transcriptomic profiling reveals global reprogramming of stress-responsive transcription factors (MYB, WRKY, bHLH) and metabolic pathways (TCA cycle, phenylpropanoid biosynthesis), while metabolomics identifies protective osmolytes (proline, trehalose) and secondary metabolites as key stress-alleviating compounds. Ionomic analysis confirms endophyte-mediated maintenance of K⁺/Na⁺ homeostasis and restricted cadmium translocation to shoots. We propose that synthetic microbial consortia combining complementary bacterial and fungal endophytes, guided by multi-omics signatures and precision gene editing, represent a viable strategy for climate-resilient agriculture in salt-affected and metal-contaminated soils.